Well I just checked your preview in SkinBuilder. I must tell you that I really can't find why your panels are not in working condition. Everything is set like it should be. You must have erased something inside skin properties or something... that's why is always best to start making skin from the scratch... now, you have big problem... I guess, best would be to load one of those existing skins in SkinBuilder and start loading your graphics all over again. I know it's painful, but believe me, making some of those skins, I had to do that sometimes even 3 times in a roll... that's why that process is not so easy.
Few errors in your skin, I've noticed...
1.) Local Disk icon has double-repeating line just below icon.. and it's not verticaly centered according to other 3 icons on the right side...
2.) Sliders inside sliding (animated) panels are way to long, and shifted to right, so they sticks out of panels...
3.) Button order is kinda confusing, but of course that's only my opinion.
Don't take this as something personal, but those are just creative comments... you asked me for opinion in the first place
Advice: Load one of existing skins and just replace all those graphics if it's not too much work for you... that way you'll avoid painful and longlasting search for existing problems in your skin... believe me, I've been there, done that... million times... remember, we are talking about SkinBuilder